Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function

Endometriosis is a leading cause of pain and infertility affecting millions of women globally. Herein, we characterize variation in DNA methylation (DNAm) and its association with menstrual cycle phase, endometriosis, and genetic variants through analysis of genotype data and methylation in endometrial samples from 984 deeply-phenotyped participants. We estimate that 15.4% of the variation in endometriosis is captured by DNAm and identify significant differences in DNAm profiles associated with stage III/IV endometriosis, endometriosis sub-phenotypes and menstrual cycle phase, including opening of the window for embryo implantation. Menstrual cycle phase was a major source of DNAm variation suggesting cellular and hormonally-driven changes across the cycle can regulate genes and pathways responsible for endometrial physiology and function. DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis, highlighting candidate genes contributing to disease risk. Our work provides functional evidence for epigenetic targets contributing to endometriosis risk and pathogenesis. Data generated serve as a valuable resource for understanding tissue-specific effects of methylation on endometrial biology in health and disease.

Description: Summary of endometriosis case and control ascertainment criteria and subphenotypes for each methylation and genetic dataset contributing to the analysis.

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Description: Phenotypic variance captured by endometrial DNAm. Proportion of variance in endometriosis case-control status captured by common genetic variants and genome-wide DNA methylation (DNAm) in endometrium estimated using different GREML and OREML models. GRM is genetic relationship matrix and ORM is omic-relationship matrix.

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Description: Values of weighted partial R2 (%) from PC-PR2 analysis indicating the proportion of variability of methylation levels, before and after correction with surrogate variables, explained by covariates.   Description: Pathway analysis of genes annotated to differentially methylated CpG sites between menstrual cycle phases. N is the total number of genes in the pathway and DM is the number of genes from the pathway that were annotated to the differentially methylated CpG sites.

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Description: Pathway analysis of genes annotated to differentially methylated CpG sites in clusters associated with menstrual cycle phase from WGCNA. N is the total number of genes in the pathway and DM is the number of genes from the pathway that were annotated to the differentially methylated CpG sites.

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Description: WGCNA Pathway Analysis. Pathway analysis of genes annotated to CpG sites in modules associated with case:control. N is the total number of genes in the pathway and DM is the number of genes from the pathway that were annotated to the differentially methylated CpG sites.

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Description: Genomic Locations of CpG sites located in WGCNA modules.

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Description: Summary statistics for potential endometrial specific mQTLs.

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Description: Pathways enriched for genes annotated to potential endometrial specific mQTLs. N is the total number of genes in the pathway and DM is the number of genes from the pathway that were annotated to the differentially methylated CpG sites.

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Description: Context specific mQTLs for menstrual cycle stage and endometriosis.

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Description: Endometrial meQTLs significantly associated with overall endometriosis and stage III/IV endometriosis using SMR. Associated eQTLs are those significantly associated with the meQTL using SMR. Associated eQTLs highlighted in red are those significantly associated with endometriosis using SMR. Enhancer and promoter evidence for each tissue/cell type is based on predicted chromatin states using the 18-state Roadmap model from histone marks (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K9me3, H3K27me3)(observed and imputed) using ChromHMM

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Description: SMR results for eQTLs significantly associated with SMR significant mQTLs.

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Description: SMR results for eQTLs significantly associated with endometriosis.

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Description: Pathways significantly enriched for genes annotated to predicted promotors and enhancers and eQTLs. N is the total number of genes in the pathway and DM is the number of genes from the pathway that were annotated to the differentially methylated CpG sites.

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Description: Summary and description of the endometriosis sub-phenotype comparisons.

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Description: Results of the 66 probes that were significantly differentially methylated in either of the 18 phenotypes including the effect-sizes, p-values from the differential methylation analysis, annotation of the probes and if any mQTLs in endometrium for these probes, the mQTL results and the LD with endometriosis GWAS loci.

File name: Supplementary Data 20
Description: Summary endometriosis cases and controls for each GWAS dataset contributing to the European GWAS meta-analysis.